In terms of difference in inner strength, the gap between Wuji and Miejue should be larger (percentage wise at least) than Xu Zhu vs Jiumozhi right?
At the point of their fight, Xu Zhu had only received Wuyazi's inner strength and had not yet absorbed the other two elders yet. Unless we believe Wuyazi is more than 4-5x stronger in inner strength than a Great level fighter like Jiumozhi (which ultimately would lead to Xu Zhu having 15x+ the inner strength of a Great later on...), the difference should be less than Wuji who is around 4-5x of Miejue at this point of the story. By the end of the novel Wuji likely has 10x the inner strength of someone like Miejue.
Neither knew how to use their inner strength at this point either; it was just the auto function that protected them.
Why is Miejue able to harm Wuji with her bare palms, while Jiumozhi was helpess against Xuzhu and was actually hurting himself? Sure Miejue used a bit of trickery in her palm techniques, but Jiumozhi is a Great level fighter who has much more at his disposal than her; he wasn't a one tricky pony that could only hit at full strength and clearly saw he was up against a terrible martial artist with great inner strength.
What's happening in these fights?
Edit: Looks like I mis-remembered actually and it was after he absorbed the 3 Elders. So nvm, it makes more sense. There is still a difference in a Greats level fighter beating himself up versus Miejue being able to hurt someone with 5x+ her inner strength, but it is explainable!